Reproducible Snakemake workflow for paired-end CUT&RUN (no spike-in): MACS2 + SEACR peak calling with matched IgG/Input controls, mode-aware consensus count matrices, ENCODE-grade QC, and opt-in DESeq2 differential binding + ChIPseeker/HOMER downstream analysis
quality-control snakemake homer epigenomics peak-calling deeptools cutandrun differential-binding chipseeker seacr motif-enrichment
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Updated
Jul 30, 2026 - Python